tbuckley/cabot-search huggingface dataset:
Abstract 6681: XNA increases assay sensitivity in sanger sequencing, qPCR, NGS and CRISPR mutant screening
Authors: Wei Liu, Robert Brown, Andrew Fu, Shuo Shen, Michael Sha, Aiguo Zhang
Journal: Cancer Research (2023)

Abstract The proprietary XNA (xeno nucleic acid) technology has wide applications in sensitive detection of rare mutations in different genomic platforms. These target-specific DNA oligo analogs increase assay sensitivity by blocking the polymerase-dependent amplification of wildtype sequence so only amplification of the mutant sequence occurs. Here we show that the XNA technology helps enrich rare somatic mutations in different human specimen types such as FFPE and plasma samples, using technology platforms such as Sanger sequencing, TaqMan qPCR, and NGS. XNA increases assay sensitivity to 0.1% for Sanger sequencing and qPCR. For NGS, XNA allows detection of the mutant sequence at a lower sequencing depth, thus combining XNA technology with NGS for MRD (molecular residual disease) detection could improve cancer management. In addition, We also show CRISPR mutant screening using a target-specific XNA in a SYBR Green qPCR assay. XNA can be used for rapid CRISPR mutant screening for DNA from pool or individual clones generated from gene editing experiments. In summary, XNA technology is a powerful tool when combined with existing genomic mutation detection platforms to screen for rare somatic mutations and for rapid CRISPR mutant screening. The technology is customizable as a service for easy integration with current technology platforms and applications. Citation Format: Wei Liu, Robert Brown, Andrew Fu, Shuo Shen, Michael Sha, Aiguo Zhang. XNA increases assay sensitivity in sanger sequencing, qPCR, NGS and CRISPR mutant screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6681.
Abstract 6654: Association PD-L1 overexpression with immune checkpoint inhibitor effect in triple-negative breast cancer
Authors: A Young Park, Ju Hee Kim, Sangen Lee, Hong Kyu Kim, Han-Byoel Lee, Wonshick Han
Journal: Cancer Research (2023)

Abstract Background: Recently, studies on the antitumor effects of PD-L1 inhibitors have gained importance in difficult to treat solid tumors. In particular, the expression of PD-L1 could be an important factor in evaluating the possibility of immunotherapy in triple-negative breast cancer where targeted therapy is not possible and the prognosis is poor. Accordingly, this study investigated the effect of PD-L1 overexpression on the immune checkpoint inhibitor effect in triple-negative breast cancer. Method: The relationship between T stage and N stage according to PD-L1 mRNA expression was analyzed in the TCGA and METABRIC datasets of breast cancer. To evaluate the role of PD-L1, PD-L1-overexpressing breast cancer cell lines for in vitro and in vivo experiments were established. Result: Using TCGA and METABRIC datasets, we found that PD-L1 showed the highest expression in breast cancer of the basal subtype, but the correlation between T stage and N stage according to PD-L1 expression was not statistically significant. To determine the functional importance of PD-L1 in breast cancer, we established 4T1-PD-L1-overexpressing breast cancer cell lines. We observed that the overexpression of PD-L1 promoted cell proliferation, migration, and invasion. In the orthotopic tumor mouse model, PD-L1 showed no significant difference in tumor growth compared to the control group, but anti-PD-L1 treatment showed a significant antitumor effect. Conclusion: We confirmed that overexpression of PD-L1 in an orthotopic breast cancer model did not induce increased tumor growth. Above all, it was confirmed that a high PD-L1 level enhances the antitumor effect of immune checkpoint inhibitors. Our findings show that the expression level of PD-L1 in breast cancer has a significant effect on the immune checkpoint inhibitor effect. We need to further investigate the role of PD-L1 in breast cancer. Citation Format: A Young Park, Ju Hee Kim, Sangen Lee, Hong Kyu Kim, Han-Byoel Lee, Wonshick Han. Association PD-L1 overexpression with immune checkpoint inhibitor effect in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6654.
Abstract 2583: AKT2 as the determining factor for PTEN loss-induced liver malignancy
Authors: Qi Tang, LIna He, Chien-Yu Chen, Shefali Chopra, Bangyan L. Stiles
Journal: Cancer Research (2023)

Abstract Liver malignancies consist of hepatocellular carcinoma (HCC) with the highest occurrence, intrahepatic cholangiocarcinoma (iCCA), and serval rare subtypes, which is the third lethal cause among all cancer types worldwide. PTEN is a well-known tumor suppressor gene, liver-specific loss of PTEN leads to the development of liver tumors from tumor-initiating cells (TICs). A mouse model that specifically mutant PTEN in hepatocytes (PM mice, PTENloxP/loxP; Alb-Cre+) has been used to mimic the natural progression of liver malignancy and study the mechanism of liver tumorigenesis. AKT, also known as protein kinase B, is a downstream kinase that is negatively regulated by PTEN. PTEN loss will unequivocally result in AKT phosphorylation and activation of the AKT pathway. In this study, we explored the role of AKT2, the most abundant liver isoform of AKT in the PTEN loss-driven liver malignancy by generating a new double mutant mouse model (DM mice, PTENloxP/loxP; AKT2loxP/loxP; Alb-Cre+). Our data demonstrated that only PM mice developed tumors starting from a 6-month age. A moderate reactive duct/oval cell accumulation phenotype is observed in the PM livers with Von Meyenbury complex (VMC) formation. And both HCC and iCCA phenotypes are observed following steatosis development in PM mice. AKT2 loss arrested tumor development at the pre-malignant stage. The DM mice also developed VMC condition with minimum steatosis starting from 9-month age and some of them manifest an advanced stage called polycystic liver disease. No tumors are observed in these mice up to 16 months of age. Our preliminary data showed that the deletion of AKT2 attenuated the accumulation of TICs marked by Sox9 suggesting a potential role of SOX9 in the regulation of PTEN-driven tumorigenesis. In summary, our result shows that AKT2 is a determining factor in PTEN loss-induced liver malignancy. Citation Format: Qi Tang, LIna He, Chien-Yu Chen, Shefali Chopra, Bangyan L. Stiles. AKT2 as the determining factor for PTEN loss-induced liver malignancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2583.
Abstract 6647: Dostarlimab shows dose-dependent immune activation of the tumor microenvironment in a patient-derived NSCLC explant model similar to pembrolizumab
Authors: Jessica Perrin, Frank Wippich, Valeriia Sherina, Dmytro Dvornikov, Katharina Lupar, Murad M. Melhem, Patrick Hanafin, Jeremy Waight, Jong Yu, Sapna Yadavilli, Daniel Poeckel, Giovanna Bergamini
Journal: Cancer Research (2023)

Abstract The ability to more faithfully mimic the tumor microenvironment (TME) of cancer patients offers a wide range of possibilities for non-clinical evaluation of anti-cancer therapeutics, including guidance for patient selection, dose, and combinations. We have established a patient-derived tumor explant (PDE) model to monitor immune activation within a structurally preserved TME, following ex vivo incubation with immune check point inhibitors (ICI). When testing anti-PD-1 agents, such as dostarlimab and pembrolizumab, in a cohort of NSCLC explants from stage I-III treatment-naïve patients, we observed that approximately half demonstrate release of inflammatory cytokines after two days incubation. Interestingly, responsive tumors presented with a high level of PD-L1 expression (high TPS), had elevated TMB, and were highly infiltrated by CD8+ T cells at baseline, in line with tumor baseline characteristics predictive of clinical response to anti-PD-1. When testing a dose-range of dostarlimab and pembrolizumab comparable potencies were observed when measuring cytokine release after treatment of the NSCLC explants. In conclusion, we describe here an in vitro patient-derived NSCLC model that mirrors the heterogeneity of patients’ response for anti-PD-1 agents observed in clinical settings, representing a valuable tool for comparative analysis of novel ICI assets and combinations, such as the CD226 axis members. Importantly, this system is also amenable to extensive multi-omics and genetics-based analyses, providing the opportunity to better identify predictive or pharmacodynamic characteristics within patient tumors. Citation Format: Jessica Perrin, Frank Wippich, Valeriia Sherina, Dmytro Dvornikov, Katharina Lupar, Murad M. Melhem, Patrick Hanafin, Jeremy Waight, Jong Yu, Sapna Yadavilli, Daniel Poeckel, Giovanna Bergamini. Dostarlimab shows dose-dependent immune activation of the tumor microenvironment in a patient-derived NSCLC explant model similar to pembrolizumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6647.
Abstract 259: Fully automated targeted sequencing sample prep on open platform liquid handlers
Authors: Ashraf Wahba, Yun Bao, Heng Wang, Kinnari Watson, Grace Q. Zhao, Shengrong Lin
Journal: Cancer Research (2023)

Abstract To accommodate the growing demands of sample throughput, reliability, and reduced hands-on time of targeted sequencing, automation is critical. The implementation of sample preparation automation is limited by several factors — complicated protocols and long incubation times. As an industry first, Avida’s Point-n-Seq™ hybridization-based targeted sequencing kit solution features 1 hr hybridization time and PCR free capture which enables full automation on a broad range of open platform liquid handlers, from the economical Opentrons (OT-2) to the high throughput Hamilton (Microlab Star). We report a walk-away targeted sequencing sample-prep solution based on the highly efficient chemistry of our Point-n-Seq technology. This strategy supports PCR-free capture for variant detection. A sequencing-ready captured library is prepared in 6 hours, with just 25 minutes of hands-on time. More importantly, a PCR-free protocol increases sequence uniformity, decreases amplicon bias as well as GC-bias, and eliminates the need for purification and quantification before capture. We have demonstrated the feasibility of automated workflows using 40 ng of genomic DNA with panel sizes ranging from 20 Kb to 2 Mb. Using a comprehensive oncology panel containing 500 genes to analyze Horizon oncology cfDNA (30 ng) or FFPE gDNA (40 ng) reference standards, we demonstrated reliable detection of SNV and structural variations with allele frequency matching the expected values. The Point-n-Seq technology enables fully automated targeted sequencing sample prep on open platform liquid handlers, enhancing accuracy and reliability while reducing hands-on time. The one hour hybridization time makes hybridization more economical on the liquid handler when compared to off-instrument for overnight/longer hybridization. This automated solution greatly accelerates the development of fast, simple, and accurate genomic profiling assays. Furthermore, Point-n-Seq targeted methylation sequencing and targeted RNA assays can also be easily adapted to the same automation platforms for research and clinical applications. Citation Format: Ashraf Wahba, Yun Bao, Heng Wang, Kinnari Watson, Grace Q. Zhao, Shengrong Lin. Fully automated targeted sequencing sample prep on open platform liquid handlers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 259.
Abstract 1740: CCR5/CCL5 axis inhibition reverses cisplatin-chemoresistance phenotye in gastric cancer cells
Authors: Priscilla Brebi, Maria Elena Reyes, Carmen Gloria Ili, Yuselin Mora, Kurt Buchegger, Ismael Riquelme, Louise Zanella, Lorena Lobos-Gonzalez, Camila Burdiles, Barbara Mora-lagos
Journal: Cancer Research (2023)

Abstract Gastric cancer (GC) is an important public health problem worldwide. Advanced GC treatment is mainly based in chemotherapy with Cisplatin (CDDP). Unfortunately, the high recurrence rate of GC is predominantly attributable to chemoresistance. The CCR5/CCL5 axis, that participates in inflammatory process, has been associated with the development and progression of cancer. However, its role in GC chemoresistance has not been fully elucidated. The objective of this work was to elucidate the role of CCR5/CCL5 axis on GC chemoresistance cells. AGS R-CDDP was established through a method based on stepwise increasing drug doses and characterized by functional assays. RNA-Sequencing (RNA-seq) was performed on Illumina HiSeq 4000. A fold change &amp;gt;2 and P&amp;lt;0.05 were used as cut-off to choose the differentially expressed genes (DEGs). Gene Ontology (GO) and signaling pathways analysis were analyzed by PANTHER. CCL5 candidate gene was validated by qRT-PCR. Signaling pathways such as STAT3, MAPK and PI3K, associated with cytokines, proliferation and survival were evaluated by western blot assays. Cell viability of CCR5/CCL5 axis inhibition was evaluated in AGS R-CDDP exposed to Chemokine receptor antagonist (CRA) alone and in combination with CDDP. Characterization studies have effectively demonstrated that AGS R-CDDP is a reliable CDDP-resistant model. Bioinformatics analyses identified a total of 189 DEGs associated mainly to molecular functions (GO) involved in CDDP-resistance. The most enriched signaling pathway was the inflammation mediated by chemokine and cytokine which could be involved in the development of CDDP resistance in GC. CCL5 was upregulated in AGS R-CDDP cells. The main signaling pathways associated with CCR5/CCL5 axis were not activated in resistant GC cells compared parental GC cells.The cytotoxicity assays showed that CRA/CDDP combination re-sensitized AGS R-CDDP cells, decreasing cell viability. Our results indicate that CCR5/CCL5 axis induce chemoresistance and CRA/CDDP combination sensitize AGS R-CDDP cells revealing its potential as coadjuvant in GC therapy. Citation Format: Priscilla Brebi, Maria Elena Reyes, Carmen Gloria Ili, Yuselin Mora, Kurt Buchegger, Ismael Riquelme, Louise Zanella, Lorena Lobos-Gonzalez, Camila Burdiles, Barbara Mora-lagos. CCR5/CCL5 axis inhibition reverses cisplatin-chemoresistance phenotye in gastric cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1740.
Abstract 3452: TNG908, a brain-penetrant MTA-cooperative PRMT5 inhibitor, is efficacious in preclinical glioblastoma models
Authors: Minjie Zhang, Alice Tsai, Kevin M. Cottrell, Brian B. Haines, Erik Wilker, Heather DiBenedetto, Ron Weitzman, Alan Huang, Charles B. Davis, John P. Maxwell, Kimberly J. Briggs
Journal: Cancer Research (2023)

Abstract Glioblastoma multiforme (GBM) is one of the most aggressive primary malignant brain tumors in adults. The median overall survival (OS) of GBM patients is poor (1-2 years) on standard of care therapies, which include surgery, radiotherapy, and the alkylating agent temozolomide. Therefore, developing new treatments for GBM is an urgent unmet medical need. TNG908 is a clinical stage MTA-cooperative PRMT5 inhibitor that inhibits PRMT5 activity selectively in MTAP-null cells leveraging a synthetic lethal interaction. Approximately 40% of GBM tumors are homozygous null for MTAP [1, 2]. In preclinical in vitro studies, the antiproliferation activity of TNG908 was 15 times more potent in MTAP-null cancer cell lines than in MTAP WT cells. TNG908 has high passive permeability and is not a substrate for P-glycoprotein nor Breast Cancer Resistant Protein efflux transporters, attributes which are favorable for crossing the blood-brain barrier. TNG908 demonstrated in vivo brain penetration in multiple preclinical studies, including non-human primates and mice, suggesting that TNG908 may fulfill the significant unmet need in the treatment of GBM. Pharmacodynamic activity of TNG908 to inhibit PRMT5 was demonstrated by decreased SDMA-modified protein levels in a dose-dependent manner in a GBM xenograft model. TNG908 demonstrated dose-dependent antitumor activity in multiple hyper- and hypomethylated GBM subcutaneous models, including cell lines and patient-derived xenograft models. Despite reduced Kpuu in rodents compared to primates, oral administration of TNG908 drove near tumor stasis and increased median survival by 3-fold in a highly aggressive murine GBM orthotopic model. In summary, TNG908 is a potent, brain-penetrant small molecule PRMT5 inhibitor that is selective for MTAP-null tumor cells with good drug-like properties and strong antitumor activity in preclinical models of GBM. As such, TNG908 may provide a novel treatment strategy for MTAP-deleted GBM patients. *MZ and AT contributed equally to the work. Reference: 1.Cerami et al., Cell, 2013. 2.Gao et al., Sci Signal, 2013 Citation Format: Minjie Zhang, Alice Tsai, Kevin M. Cottrell, Brian B. Haines, Erik Wilker, Heather DiBenedetto, Ron Weitzman, Alan Huang, Charles B. Davis, John P. Maxwell, Kimberly J. Briggs. TNG908, a brain-penetrant MTA-cooperative PRMT5 inhibitor, is efficacious in preclinical glioblastoma models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3452.
Abstract 1450: Global changes in RBPs and mRNA interactions during prostate cancer progression
Authors: Abdulrahman M. Dwead, Marwah M. Al-Mathkour, Bekir Cinar
Journal: Cancer Research (2023)

Abstract Prostate cancer (PC) is a leading cause of cancer in men in the United States and worldwide, disproportionately affecting men of African ancestry. The etiology and molecular mechanism contributing to lethal human PC remain poorly understood. RNA binding proteins (RBPs) controlled all aspects of RNA biogenesis, and dysregulated RBPs are linked to human diseases, including cancer. However, the global changes in RBP-mRNA interactions during PC progression are unknown. Here, we have investigated the patterns of RBPs and polyA-mRNA interaction in the castration-sensitive LNCaP and castration-resistant C4-2 PC cell lines. Our enhanced-RNA interactome capture assay combined with mass spectroscopy (MS) revealed that LNCaP and C4-2 cells showed distinct RBP-mRNA interaction patterns in steady-state and androgen-treated conditions. Also, we have studied the interaction between Yes-associated protein 1 (YAP1) and nucleophosmin (NPM1) RBP. Androgen increased NPM1 and mRNA interaction, and NPM1 is part of the YAP1 multiprotein complex, as revealed by MS-based proteomics approaches. Our proximity ligation assay showed that androgen hormone signaling regulated the interaction between YAP1 and NPM1. Besides, our GST-pulldown demonstrated that NPM1 binds the proline-rich region domain of YAP1, whereas the WW/SH3 domain of YAP1 mediates the interaction in C4-2 cells. Genetic silencing of NPM1 reduced PC cell growth in culture. Furthermore, the upregulation of NPM1 correlates with prostate adenocarcinoma and metastasis. These observations suggest that changes in RBP and RNA interaction patterns may play a critical role in PC progression and recurrence. Citation Format: Abdulrahman M. Dwead, Marwah M. Al-Mathkour, Bekir Cinar. Global changes in RBPs and mRNA interactions during prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1450.
Abstract 2584: Overcoming cetuximab resistance in colorectal cancer through inhibition of HGF processing
Authors: Vivian Truong Jones, Ramona Graves-Deal, Galina Bogatcheva, Zheng Cao, James Higginbotham, Sarah Harmych, Gregory Ayers, Marisol Ramirez, Qi Liu, James Janetka, Bhuminder Singh
Journal: Cancer Research (2023)

Abstract Cetuximab is a monoclonal antibody against epidermal growth factor receptor (EGFR) and can prolong survival in metastatic colorectal cancer (CRC) patients. However, therapeutic resistance can limit its efficiency and use. Our lab has previously identified that the activation of receptor tyrosine kinases (RTKs) MET and RON contributed to cetuximab resistance. In the absence of activating mutations of MET and RON, the activity of these RTKs depends on the availability of their ligands, hepatocyte growth factor (HGF) and hepatocyte growth factor-like (HGFL), respectively. To become biologically active, the inactive precursors of HGF and HGFL must be processed by serine proteases (HGFA, matriptase, and hepsin). A survey of TCGA datasets indicated that MET and HGF were overexpressed in several CRC CMS subtypes. However, we did not observe any significant overexpression of the serine proteases. Hepatocyte growth factor activator inhibitor type 1 and 2 (HAI-1/2) are two Kunitz-type serine protease inhibitors that displayed reduced expression in TCGA datasets. The addition of recombinant human HGF conferred cetuximab resistance to cetuximab-sensitive cells and cetuximab-sensitive cells engineered to overexpress HGF also exhibited cetuximab-resistant phenotype. Cetuximab resistance induced by HGF addition or overexpression could be overcome by downstream inhibition with crizotinib, a multi-targeted RTK inhibitor. ZFH7116 is a small molecule inhibitor of the serine proteases that mimics HAI-1 activity. ZFH7116 suppressed HGF cleavage and maturation in our cetuximab-resistant SC cells. We observed cooperative effect of ZFH7116 with cetuximab to reduce SC cell growth in 3D collagen cultures. We are currently testing if upstream inhibition with recombinant human HAI-1 addition can suppress HGF cleavage and overcome cetuximab resistance induced by HGF overexpression. Collectively, our findings suggest that inhibiting HGF cleavage and processing may be a unique strategy for overcoming EGFR-targeted therapy resistance in colorectal cancer. Citation Format: Vivian Truong Jones, Ramona Graves-Deal, Galina Bogatcheva, Zheng Cao, James Higginbotham, Sarah Harmych, Gregory Ayers, Marisol Ramirez, Qi Liu, James Janetka, Bhuminder Singh. Overcoming cetuximab resistance in colorectal cancer through inhibition of HGF processing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2584.